Microbial Carbon Flux Research Articles

Modeling microbial carbon fluxes and stocks in global soils from 1901 to 2016

Abstract. Soil microbes play a crucial role in the carbon (C) cycle; however, they have been overlooked in predicting the terrestrial C cycle. We applied a microbial-explicit Earth system model – the Community Land Model-Microbe (CLM-Microbe) – to investigate the dynamics of soil microbes during 1901 to 2016. The CLM-Microbe model was able to reproduce the variations of gross (GPP) and net (NPP) primary productivity, heterotrophic (HR) and soil (SR) respiration, microbial (MBC) biomass C in fungi (FBC) and bacteria (BBC) in the top 30 cm and 1 m, and dissolved (DOC) and soil organic C (SOC) in the top 30 cm and 1 m during 1901–2016. During the study period, simulated C variables increased by approximately 12 PgC yr−1 for HR, 25 PgC yr−1 for SR, 1.0 PgC for FBC and 0.4 PgC for BBC in 0–30 cm, and 1.2 PgC for FBC and 0.7 PgC for BBC in 0–1 m. Increases in microbial C fluxes and pools were widely found, particularly at high latitudes and in equatorial regions, but we also observed their decreases in some grids. Overall, the area-weighted averages of HR, SR, FBC, and BBC in the top 1 m were significantly correlated with those of soil moisture and soil temperature in the top 1 m. These results suggested that microbial C fluxes and pools were jointly governed by vegetation C input and soil temperature and moisture. Our simulations revealed the spatial and temporal patterns of microbial C fluxes and pools in response to environmental change, laying the foundation for an improved understanding of soil microbial roles in the global terrestrial C cycle.

Saharan Dust Pulse and High Ultraviolet Radiation Alter Microbial Carbon Fluxes in the South-Western Mediterranean Sea

Saharan Dust Pulse and High Ultraviolet Radiation Alter Microbial Carbon Fluxes in the South-Western Mediterranean Sea

Drivers of Microbial Carbon Fluxes Variability in Two Oligotrophic Mediterranean Coastal Systems

The carbon fluxes between phytoplankton and heterotrophic bacterioplankton were studied in two coastal oligotrophic sites in the NW Mediterranean. Phytoplankton and bacterial production rates were measured under natural conditions using different methods. In the Bay of Villefranche, the temporal variability revealed net heterotrophy in July-October and net autotrophy in December-March. The spatial variability was studied in the Bay of Palma, showing net autotrophic areas in the west and heterotrophic areas in the east. On average bacterial respiration, represented 62% of the total community respiration. Bacterial growth efficiency (BGE) values were significantly higher in autotrophic conditions than in heterotrophic ones. During autotrophic periods, dissolved primary production (DPP) was enough to sustained bacterial metabolism, although it showed a positive correlation with organic carbon stock (DOC). Under heterotrophic conditions, DPP did not sustain bacterial metabolism but bacterial respiration correlated with DPP and bacterial production with DOC. Temperature affected positively, DOC, BGE, bacterial respiration and production when the trophic status was autotrophic. To summarize, the response of bacterial metabolism to temperature and carbon sources depends on the trophic status within these oligotrophic coastal systems.

The effect of temperature increase on microbial carbon fluxes in the Adriatic Sea: an experimental approach.

An assessment of the temperature increase effect on processes within the microbial food web provides a better insight into the carbon transfer and energy flow processes in marine environments in the global warming perspective. Modified laboratory dilution experiments that allow simultaneous estimates of protozoan grazing and viral lysis on picoplankton groups (bacteria, Prochlorococcus, Synechococcus and pico-eukaryotic algae) under in situ and 3°C above in situ temperatures were performed at seasonal scale. Picoplankton mortality due to grazing was generally higher than that caused by viral lysis, especially in the cold months. The largest part of HNF carbon demand was satisfied by grazing on bacteria throughout the year. Although ciliates satisfied their carbon demand predominantly through grazing on HNF and bacteria, the role of autotrophic picoplankton (APP) as their prey increased significantly in the cold months. Bacteria constituted the most important host for viruses throughout the year. However, during the warm months, APP groups were also significant hosts for viral infection. Under the warming condition the amount of picoplankton biomass transferred to protozoan grazers exceeded the lysed biomass, suggesting that global warming could further increase picoplankton carbon flow toward higher trophic levels in the Adriatic Sea.

Large Plankton Enhance Heterotrophy Under Experimental Warming in a Temperate Coastal Ecosystem

Microbes are key players in oceanic carbon fluxes. Temperate ecosystems are seasonally variable and thus suitable for testing the effect of warming on microbial carbon fluxes at contrasting oceanographic conditions. In four experiments conducted in February, April, August and October 2013 in coastal NE Atlantic waters, we monitored microbial plankton stocks and daily rates of primary production, bacterial heterotrophic production and respiration at in situ temperature and at 2 and 4°C over ambient values during 4-day incubations. Ambient total primary production (TPP) exceeded total community respiration (< 200 µm, TR) in winter and fall but not in spring and summer. The bacterial contribution to ecosystem carbon fluxes was low, with bacterial production representing on average 6.9 ± 3.2% of TPP and bacterial respiration (between 0.8 and 0.2 µm) contributing on average 35 ± 7% to TR. Warming did not result in a uniform increase in the variables considered, and most significant effects were found only for the 4°C increase. In the summer and fall experiments, under warm and nutrient-deficient conditions, the net TPP/TR ratio decreased by 39 and 34% in the 4°C treatment, mainly due to the increase in respiration of large organisms rather than bacteria. Our results indicate that the interaction of temperature and substrate availability in determining microbial carbon fluxes has a strong seasonal component in temperate planktonic ecosystems, with temperature having a more pronounced effect and generating a shift toward net heterotrophy under more oligotrophic conditions as found in summer and early fall.

Impact of short-term warming on seasonal variations in bacterial growth, grazing, and viral lysis in coastal waters of Taiwan

Although temperature is a key parameter controlling the activity and growth of all microorganisms, information about how water temperature may affect the trophic interactions and carbon flow patterns of microbial food webs is not consistent. We investigated the response in bacterial gross growth, grazing rates, and viral lysis to small temperature changes (3°C above in situ values) in coastal waters of Taiwan using a modified dilution method approach over a 1 yr period from September 2013 to September 2014. Warming increased the bacterial gross growth rates and bacterial losses to grazing, demonstrating clear seasonality. The warming conditions led to a 5 to 200% increase in bacterial gross growth rates. The increase ratios of bacterial gross growth rates were low (5 to 25%) at higher ambient temperatures (>25°C) but increased exponentially at lower ambient temperatures (<25°C) with warming. Grazing increased in parallel with seasonal bacterial growth, while viral lysis did not. These results could prove useful in forming a testable hypothesis about the possible directions of change of microbial carbon fluxes that may accompany the warming of the coastal waters of Taiwan.

Towards a better understanding of microbial carbon flux in the sea*

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 53:21-38 (2008) - DOI: https://doi.org/10.3354/ame01230 AME Special: 'Progress and Perspectives in Aquatic Microbial Ecology: Highlights of the SAME 10, Faro, Portugal, September 2007' Towards a better understanding of microbial carbon flux in the sea* Josep M. Gasol1,**, Jarone Pinhassi2,**, Laura Alonso-Sáez3, Hugh Ducklow4, Gerhard J. Herndl5, Michal Koblízek6, Matthias Labrenz7, Yawei Luo4, Xosé Anxelu G. Morán4,8, Thomas Reinthaler5, Meinhard Simon9 1Institut de Ciències del Mar-CSIC, Pg. Marítim de la Barceloneta 37–49, 08003 Barcelona, Catalunya, Spain 2School of Pure & Applied Natural Sciences, University of Kalmar, 39182 Kalmar, Sweden 3Department of Ecology & Evolution, Limnology group, Uppsala University, PO Box 573, 75123 Uppsala, Sweden 4The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA 5Dept. Biological Oceanography, Royal Netherlands Institute for Sea Research (Royal NIOZ), PO Box 59, 1790 AB Den Burg, The Netherlands 6Institute of Microbiology CAS, Opatovick´y ml´yn, 379 81 Trebon and Institute of Physical Biology JU, Zámek 136, 373 33 Nové Hrady, Czech Republic 7IOW-Leibniz Institute for Baltic Sea Research, Seestrasse 15, 18119 Rostock-Warnemünde, Germany 8Centro Oceanográfico de Xixón, Instituto Español de Oceanografía, Camín de L’Arbeyal, s/n, 33212 Xixón, Spain 9Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany *All authors contributed equally to this paper**Emails: pepgasol@icm.csic.es, jarone.pinhassi@hik.se ABSTRACT: We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas. KEY WORDS: Carbon flux · Microbial ecology · Ocean · Bacteria · Protists · Light · Genomics · Chemoautotrophy · Models Full text in pdf format PreviousNextCite this article as: Gasol JM, Pinhassi J, Alonso-Sáez L, Ducklow H and others (2008) Towards a better understanding of microbial carbon flux in the sea*. Aquat Microb Ecol 53:21-38. https://doi.org/10.3354/ame01230Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 53, No. 1. Online publication date: September 18, 2008 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2008 Inter-Research.

Zinc induces shifts in microbial carbon flux in tropical coastal environments

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 52:57-68 (2008) - DOI: https://doi.org/10.3354/ame01212 Zinc induces shifts in microbial carbon flux in tropical coastal environments E. J. Rochelle-Newall1,3,*, B. Delesalle2, X. Mari1, C. Rouchon1, J.-P. Torréton1,3, O. Pringault1 1UR 103, CAMELIA, Centre IRD Nouméa, BP A5, 98848 Nouméa, New Caledonia 2Biologie et Ecologie Tropicale et Méditerranéenne, UMR 5244 CNRS - EPHE - UPVD, Université Via Domitia, 52 avenue Paul Alduy, 66860 Perpignan, France 3Present address: ECOLAG, UR103/UMR5119, Université Montpellier II, Case 093, 34095 Montpellier, France *Email: emma.rochelle-newall@ird.fr ABSTRACT: A great deal of research has been conducted in temperate coastal ecosystems in order to understand the effect of anthropogenic inputs on the structure and function of the system; however, despite the fact that many tropical ecosystems are subject to increasing anthropogenic pressure, including increased nutrient and contaminant inputs, less attention has been paid to tropical regions. We present the results from a series of experiments aimed at examining the effects of Zn on microbial carbon fluxes in a tropical coastal ecosystem. We show that Zn additions at concentrations lower than the clean water limits set by environmental protection agencies for tropical waters can result in considerable changes in microbial carbon cycling in both the structure and function of the auto- and heterotrophic compartments. We observed a reduction in the relative proportion of diatoms and a concomitant increase in the relative proportions of other phytoplankton, notably dinoflagellates. Zn contamination resulted in a 2-fold increase in the amount of total primary production incorporated into bacterial biomass. This was concomitant with a reduction in the P:R ratio in the presence of Zn and ultimately resulted in a bacterially dominated, heterotrophic system. This shift in balance between production and respiration further pushes the system towards being a carbon source to the atmosphere rather than a sink. These results show that even low concentrations of Zn can have a negative effect on the lower levels of the food web and on carbon transfer in sensitive coastal environments. KEY WORDS: Zn · Bacteria · Percentage of extracellular release · PER · Primary production · Tropical coastal systems Full text in pdf format PreviousNextCite this article as: Rochelle-Newall EJ, Delesalle B, Mari X, Rouchon C, Torréton JP, Pringault O (2008) Zinc induces shifts in microbial carbon flux in tropical coastal environments. Aquat Microb Ecol 52:57-68. https://doi.org/10.3354/ame01212 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 52, No. 1. Online publication date: June 26, 2008 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2008 Inter-Research.

Production process monitoring by serial mapping of microbial carbon flux distributions using a novel sensor reactor approach: I—Sensor reactor system

A novel Sensor Reactor technology is presented which permits 13C labeling experiments for metabolic flux analysis during large-scale, semi-industrial, (fed-) batch fermentation processes deriving a series of flux maps that document fermentation courses in detail. The small-scale Sensor Reactor can be inoculated within 1.50–1.20 s via a special inoculation unit with an inoculation volume accuracy of 1.025±0.021 L. The large-scale production reactor (here: 300 L) and the Sensor Reactor were run in parallel master/slave modes to control the current pH, temperature, pressure and dissolved oxygen values as changing set points for the Sensor Reactor. Using an automated pulsing technology, glucose pulses of 5 g/L could be realized within 0.51 s. The similarity of fermentations in the Sensor Reactor with the production process was demonstrated by studying l-lysine production with C. glutamicum during multiple, ‘simulated’ labeling experiments each lasting 2.5 h. ‘Real’ labeling experiments are presented in Part II.

Production process monitoring by serial mapping of microbial carbon flux distributions using a novel Sensor Reactor approach: II— 13C-labeling-based metabolic flux analysis and l-lysine production

Corynebacterium glutamicum is intensively used for the industrial large-scale (fed-) batch production of amino acids, especially glutamate and lysine. However, metabolic flux analyses based on 13C-labeling experiments of this organism have hitherto been restricted to small-scale batch conditions and carbon-limited chemostat cultures, and are therefore of questionable relevance for industrial fermentations. To lever flux analysis to the industrial level, a novel Sensor Reactor approach was developed (El Massaoudi et al., Metab. Eng., submitted), in which a 300-L production reactor and a 1-L Sensor Reactor are run in parallel master/slave modus, thus enabling 13C-based metabolic flux analysis to generate a series of flux maps that document large-scale fermentation courses in detail. We describe the successful combination of this technology with nuclear magnetic resonance (NMR) analysis, metabolite balancing methods and a mathematical description of 13C-isotope labelings resulting in a powerful tool for quantitative pathway analysis during a batch fermentation. As a first application, 13C-based metabolic flux analysis was performed on exponentially growing, lysine-producing C. glutamicum MH20-22B during three phases of a pilot-scale batch fermentation. By studying the growth, (co-) substrate consumption and (by-) product formation, the similarity of the fermentations in production and Sensor Reactor was verified. Applying a generally applicable mathematical model, which included metabolite and carbon labeling balances for the analysis of proteinogenic amino acid 13C-isotopomer labeling data, the in vivo metabolic flux distribution was investigated during subsequent phases of exponential growth. It was shown for the first time that the in vivo reverse C 4-decarboxylation flux at the anaplerotic node in C. glutamicum significantly decreased (70%) in parallel with threefold increased lysine formation during the investigated subsequent phases of exponential growth.